Molecular Ecology (2007) 16, 3759–3767 doi: 10.1111/j.1365-294X.2007.03439.x

Blackwell Publishing LtdOPINION ARTICLE

Cross-species transfer of nuclear microsatellite markers: potential and limitations

THELMA BARBARÁ,* CLARIS SE PA LMA-S ILVA,† GECELE M. PAG GI,† FERNA NDA BERED,† MICHA EL F. FAY* and CHRIS TIAN LEXER**Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, Surrey TW9 3DS, UK, †Departamento de Genética — IB/UFRGS — Av. Bento Gonçalves, 9500 Porto Alegre–RS, 91501-970, Brazil

Abstract

Molecular ecologists increasingly require ‘universal’ genetic markers that can easily be transferred between species. The distribution of cross-species transferability of nuclear microsatellite loci is highly uneven across taxa, being greater in animals and highly variablein flowering plants. The potential for successful cross-species transfer appears highest in species with long generation times, mixed or outcrossing breeding systems, and where genome size in the target species is small compared to the source. We discuss the implica-tions of these findings and close with an outlook on potential alternative sources of cross-species transferable markers.

Keywords: animals, cross-species amplification, DNA sequencing, fungi, microsatellites, plants

Received 20 March 2007; revision accepted 25 May 2007

Nuclear microsatellites are currently one of the most popular types of genetic markers for molecular ecology studies. However, molecular ecologists increasingly require universal markers that can readily be transferred between species. Such transferable markers facilitate comparisons among closely related taxa for addressing the mechanisms involved in population divergence and speciation (Noor & Feder 2006), and comparisons among multiple co-occurring species for studying how patterns of diversity at the genetic and community levels interact (Whitham et al. 2006).

Ongoing research on the genetic effects of habitat frag-mentation in a biodiversity ‘hotspot’, the Atlantic Rainfor-est of Brazil (Myers et al. 2000), has confronted us with an issue well known to readers of this journal: many species need to be studied in a comparative way while time to do so is running out, in our case due to logging and urban development which reduce remaining forest fragments at a rapid pace. This has prompted us to utilize the potential of cross-species transfer of microsatellite loci in our ongo-ing studies (Palma-Silva et al. 2006; Barbará et al. 2007). It has also led us to investigate its potential in other taxa to inform molecular ecologists in similar situations, and the results of our literature search are discussed here. We do

not focus on interspecific differences in microsatellite muta-tion rates, constraints on microsatellite evolution, or homo-plasy, as these issues have been dealt with elsewhere (e.g. Estoup & Cornuet 1999; Amos 1999). Rather, we focus on the likelihood of successful cross-species transfer meas-ured as the proportions of amplified and polymorphic markers in a large number of animals, fungi, and plants. In doing so, we expand earlier studies by Schlötterer et al. (1991), Primmer et al. (1996, 2005), Rosetto (2001), and Primmer & Merilä (2002) on the conservation of micro-satellite loci in specific groups of taxa. To our knowledge, this is the first comprehensive evaluation of microsatellite cross-species transfer potential across three kingdoms.

Review of the success of cross-species marker transfer in animals, plants, and fungi

We reviewed 64 primer notes published in Molecular Ecology, Molecular Ecology Notes, and elsewhere between 1997 and mid-2006, representing a total of 611 cross-species encounters and matching with stringent quality criteria (Table 1). Each study reported cross-transfer results for at least 10 markers and five target taxa within a fully informative table (not just partial presentation in the text). In each original study, successful marker amplification was determined by comparison to expected fragment size and/

Correspondence: Christian Lexer, Fax: +44 (0)2083325310; E-mail: c.lexer@kew.org

© 2007 The AuthorsJournal compilation © 2007 Blackwell Publishing Ltd

3760 BA R BA R A ET AL .

or direct sequencing of amplified fragments. For each cross-species encounter in each study, we scored the ‘percentage of markers amplified’ and, among those, the ‘percentage of polymorphic markers’ as surrogates of transfer success. Then we sought to explain variation in cross-species transfer success in a three-step procedure.

In the first step, we used ‘taxonomic grouping’ and the ‘taxonomic range’ of cross-species transfer as predictor variables in linear models to inspect the taxonomic distribu-tion of cross-species transfer success (see Table 2 for a key to these variables). The use of taxonomic variables rather than genetic distance based on DNA sequence data was necessary because there is currently no universal molecular ‘barcode’ across animals, fungi, and plants (Chase et al. 2005). The response of marker transfer success to taxo-nomic predictors was modelled using either least-squares analysis of variance (anova) or a mixed model including ‘source species’ of microsatellites as a random factor. The latter approach takes into account the lack of independence in cross-species comparisons involving the same source species. In the second step, we added organismal and geo-graphical predictor variables to refine the analysis and identify additional patterns. The following organismal and geographical variables were analysed: mating system, geographical distribution, distribution range, and genera-tion time (see Table 2 for factor levels of these variables). We focused on organismal factors rather than molecular properties of individual loci, as the latter have been dealt with in a review of selected animal taxa recently (Primmer et al. 2005). The organismal factors we recorded may be related to rates of molecular evolution which are known to vary greatly between taxa (Zhang & Hewitt 2003). We did

not include primer annealing temperature (Ta) in the anal-ysis because lowering Ta in cross-species amplifications is now routine. Also, no contrast between anonymous and expressed sequence tag (EST)-derived markers was intended, as this topic has been addressed elsewhere (Pashley et al. 2006; Bouck & Vision 2007). Response to organismal and geographical factors was modelled by least-squaresanova, because the representation of some of the variables was not sufficiently balanced for running mixed models, and our earlier results showed that the results of both approaches are comparable. For graphical representation, means and standard errors of transfer success for different categories of organismal/geographical factors were plotted after adjusting for differences in the taxonomic range of marker transfer. Residuals from simple one-way anovawith taxonomic range as factor variable were used for this adjustment. In a third and final step, the effect of variation in genome size (C value) on cross-species transfer success was analysed using Pearson’s correlation.

Distribution of cross-species transfer success

The results of our analysis contain information on the distribution of the effort invested by the molecular ecology community in testing the potential for cross-species marker transfer, the taxonomic distribution of cross-species transfer success that follows from these tests, and the relationship between transfer success and key organismal and geographical factors.

With respect to distribution of investment, it seems clear that the potential of cross-species marker transfer has been utilized the least where it is needed most: innarrowly endemic and tropical taxa. Our review of 64 informative primer note articles published over a 10-year period revealed only 88 cross-species encounters for tropical target taxa vs. 243 for temperate ones (Table 2 —second column from the left), despite the fact that approx-imately half of the source species in the reviewed studies were tropical. Likewise, our review revealed only 42 cross-species encounters for narrow endemics vs. 250 forwidespread and 96 for regionally distributed taxa (Table 2). The under-representation of endemic taxa is surprising,as endemics should be of great interest to conservation biologists. We suspect that failure to test the transferabilityof markers in narrow endemics is primarily due to thedifficulty of obtaining samples from suitable specimensfor the necessary laboratory tests at short notice.

With respect to taxonomic distribution of transfersuccess, we found a significant effect of ‘taxonomic group’ and, as expected from previous reports (e.g. Primmer et al. 1996; Steinkellner et al. 1997), ‘taxonomic range of marker assay’ on the proportions of amplified and polymorphic markers (Table 3). Reptiles, birds, mammals, and inverte-brates other than arthropods clearly fared best within

Table 1 Summary of the reviewed studies, including the total number of studies, total number of cross-species encounters, and number of cross-species encounters for different taxonomic categories and taxonomic ranges of molecular marker assays

Category No. of items

Total studies* 64Total cross-species encounters 611Cross-species encounters per taxonomic category: Vertebrates 311 Invertebrates 114 Plants 155 Fungi 31Taxonomic range of cross-species amplification†: Among species — within genus 301 Among genera — within family 190 Among families — within order 92 Among orders — within class 21

*Each article reported a cross-amplification table based on at least 10 markers and five target taxa. †Seven cases were difficult to classify and are thus not listed.

© 2007 The AuthorsJournal compilation © 2007 Blackwell Publishing Ltd

CR O S S - S P EC I E S T R A N S F E R O F M I C RO S AT E LL I TE S 3761

© 2007 The AuthorsJournal compilation © 2007 Blackwell Publishing Ltd

Table 2 Percentages of amplified and polymorphic markers by taxonomic group, taxonomic range of cross-species amplification, mating system, geographical distribution, distribution range, and generation time

Variable

Amplification*** Polymorphism

n†††

%

n†††

%

Mean ± SE Median Mean ± SE Median

Taxonomic group Conifers* 5 71 ± 6 66 0 — — Monocots† 23 58 ± 7 64 9 27 ± 7 35 Eudicots‡ 127 71 ± 2 80 49 48 ± 4 46 Mammals§ 84 64 ± 4 82 68 52 ± 4 61 Birds¶ 100 53 ± 3 59 38 44 ± 6 41 Reptiles** 5 85 ± 4 88 5 69 ± 11 76 Fishes†† 122 57 ± 2 58 68 57 ± 3 57 Arthropods‡‡ 95 61 ± 3 63 65 62 ± 3 65 Other invertebrates§§ 19 72 ± 7 88 9 77 ± 7 83 Fungi¶¶ 31 36 ± 7 20 0 — —

Taxonomic range Between species/within genus 301 73 ± 1 82 175 65 ± 2 67 Between genera/within family 190 60 ± 2 59 96 43 ± 3 42 Between families/within order 92 33 ± 3 25 38 28 ± 6 0 Between orders/within class 21 6 ± 2 0 0 — —

Mating system Primarily selfing 14 54 ± 9 55 5 69 ± 11 76 Mixed 162 65 ± 2 77 67 51 ± 3 49 Outcrossing 405 59 ± 2 62 238 54 ± 2 60 Unknown 30 60 ± 5 59 1 — —

Geographical distribution Tropical 88 59 ± 3 56 39 41 ± 5 33 Tropical-temperate 143 62 ± 3 64 87 57 ± 3 63 Temperate 243 59 ± 2 62 112 58 ± 3 63 Temperate-polar 36 56 ± 5 61 22 56 ± 6 58 Tropical-temperate-polar 19 44 ± 7 46 9 25 ± 11 17 Unknown 82 70 ± 3 79 42 55 ± 4 48

Distribution range Narrowly endemic 42 69 ± 5 79 25 59 ± 6 64 Regional 96 58 ± 3 57 44 55 ± 5 56 Widespread 250 56 ± 2 58 123 50 ± 3 55 Unknown 223 65 ± 2 74 119 56 ± 3 57

Generation time Annual/semelparous 64 66 ± 3 67 31 63 ± 4 63 Perennial/iteroparous 436 59 ± 2 62 213 53 ± 2 57 Unknown 112 64 ± 3 74 67 53 ± 4 56

*Conifers: Chagne et al. 2004. †Monocots: Blum et al. 2004; Flanagan et al. 2006; Tostain et al. 2006. ‡Eudicots: Steinkellner et al. (1997); White & Powell (1997); Lanaud et al. (1999); Combes et al. 2000; Squirrell & Wolff 2001; Hale et al. 2002; Escribano et al. 2004; Jones et al. 2004; Morillo et al. 2004; Topinka et al. 2004; Perez et al. 2006; Porter et al. 2006; Terui et al. 2006; Salywon & Dierig 2006. §Mammals: Gemmell et al. (1997); Ortega et al. 2002; Williamson et al. 2002; Gaur et al. 2003; Dawson et al. 2004; Maudet et al. 2004; Gunn et al. 2005. ¶Birds: Richardson et al. 2000; Chbel et al. 2002; Martinez-Cruz et al. 2002; Maak et al. 2003; Dawson et al. 2005; Mcrae et al. 2005; Rubenstein 2005. **Reptiles: Sinclair et al. 2006. ††Fishes: Cairney et al. 2000; Iyengar et al. 2000; Farias et al. 2003; Keeney & Heist 2003; Rodriguez et al. 2003; Yue et al. 2003; Lippe et al. 2004; Rogers et al. 2004; Coulibaly et al. 2005; Feulner et al. 2005; Holmen et al. 2005; Perry et al. 2005; Vasemagi et al. 2005; Ovenden et al. 2006; Tonnis 2006. ‡‡Arthropods: Belfiore & May 2000; Mohra et al. 2000; Zhu et al. 2000; Daly et al. 2002; Flanagan et al. 2002; Huttunen & Schotterer 2002; Dawson et al. 2003; Funk et al. 2006; Mavarez & Gonzalez 2006; Schug et al. 2004; Shearman et al. 2006; Smith et al. 2005. §§Other invertebrates: Eackles & King 2002; McMullin et al. 2004. ¶¶Fungi: Slippers et al. 2004; Wadud et al. 2006. ***Successful marker amplification in individual studies was inferred by comparison to expected fragment size and/or direct sequencing of amplified fragments. †††Sample sizes (n) refer to the number of cross-species encounters assessed for marker amplification and, among those that amplified, for marker polymorphism. Sample sizes are generally smaller for marker polymorphism because they represent a subset of the samples assessed for amplification, and because not all reviewed studies tested for polymorphism. SE, standard error.

3762 BA R BA R A ET AL .

genera in terms of ‘per cent markers amplified’ (Fig. 1A). The drop in transfer success to the next level (between genera/within family) was steeper for invertebrates and birds compared to reptiles and mammals, but in birds, an appreciable percentage of markers amplified successfully even between different families (Fig. 1A). The observed patterns are largely consistent with earlier observations by Schlötterer et al. (1991), Primmer et al. (1996, 2005), Rosetto (2001), and Primmer & Merilä (2002) on specific groups of taxa although, to our knowledge, cross-transferability has never been compared across taxa and kingdoms on this scale. A conspicuous pattern in plants is the greatly reduced chance of successful amplification in monocots compared to eudicots (Fig. 1A). Although observations for fungi were available only for the extremes of the taxonomic range of marker transfer, success rates appear to be intermediate and within the range of other groups of taxa (Fig. 1A). When transfer success was scored as ‘per cent polymorphic mark-ers’, then birds, reptiles, mammals, fishes, and invertebrates other than arthropods fared best within and between genera (Fig. 1B). Plants clearly fared worse than animals, again with greater transfer success in eudicots than in monocots.

Can organismal or geographical attributes of each taxon predict cross-species transfer success? As visible from the anova shown in Table 4, taxonomic range and taxonomic group clearly explained a greater proportion of the varia-tion than any other factor. Nevertheless, we found a signif-icant effect of mating system and generation time on the

per cent of amplified markers (Table 4), with lower ampli-fication success in primarily selfing and short-lived (annual or semelparous) species in our data set (Fig. 2A, D). Lower success rates in selfing species may be explained by a greater likelihood of selfers to accumulate mutations because of smaller effective population size (Ne) (Higgins & Lynch 2001; Lynch & Conery 2003). This may involve transposition, chromosomal rearrangements, local inser-tion/deletions, or point mutations, all of which could affect conservation of the markers. We note that modes and rates of genome turnover in flowering plants appear to be strik-ingly different from those observed in animals (Lim et al. 2007). Still, our result must be interpreted with care as sam-ple sizes for this particular comparison were unbalanced (Table 2; Table 4). Lower amplification success in annual or semelparous species may be explained by the direct effect of generation time or by indirect effects of differences in metabolic rates (Gillooly et al. 2005). We also found a signif-icant negative effect of genome size (C value) on cross-species amplification success (Fig. 3). Thus, genome size may not only affect the amplification of microsatellite markers in the source taxon (Garner 2002), but also the success of marker transfer between species. The great variation in amplification success at intermediate genome size ratios in the middle of the graph shown in Fig. 3 is primarily due to fishes (Salmonidae, Carcharhinidae, Clariidae, Scoph-thalmidae) and reflects large differences in the taxonomic range of cross-species marker transfer in this group.

Table 3 anova of the effects of taxonomic group, taxonomic range of marker assay, and interaction between these factors on the percentage of markers amplified (A) and the percentage of markers polymorphic (B) in cross-species amplification testsA. Percentage markers amplified

B. Percentage markers polymorphic

Source of variation*

General linear model

F P value

Mixed model†

d.f. SS MS F P value

Taxonomic group 9 126.41 14.05 5.89 0.000 13.07 0.000Taxonomic range of marker assay 3 375.40 125.13 52.45 0.000 49.60 0.000Taxonomic group × range of assay 11 58.33 5.30 2.22 0.012Error 580 1383.83 2.39

Source of variation*

General linear model

F P value

Mixed model†

d.f. SS MS F P value

Taxonomic group 7 97.77 13.97 5.71 0.000 5.63 0.000Taxonomic range of marker assay 2 111.37 55.69 22.77 0.000 19.44 0.000Taxonomic group × range of assay 8 53.13 6.64 2.72 0.007Error 291 711.55 2.45

The residuals of both models were weighted by the number of markers assayed in each study. Significant factors at the 0.05 level are indicated with bold type. *For key to taxonomic predictor variables see Table 2. †In mixed models, taxonomic predictor variables were nested within the random factor ‘microsatellite source species’ and significance was tested using maximum-likelihood estimation. d.f.: degrees of freedom; SS: sums of squares; MS: mean squares.

© 2007 The AuthorsJournal compilation © 2007 Blackwell Publishing Ltd

CR O S S - S P EC I E S T R A N S F E R O F M I C RO S AT E LL I TE S 3763

All our observations on organismal/geographical variables are for transfer success in terms of marker amplification —no significant effect on polymorphism was found. This suggests that differences in polymorphism upon cross-species transfer are either due to factors not included in our review, or to multiple factors with individual effects too small to be detected here. Reduced marker polymorphism upon cross-species transfer has often been attributed to ‘ascertainment bias’ whereby a microsatellite chosen to be maximally long in the source species is then likely to be shorterin a new target species (Ellegren et al. 1995). It is thought that ascertainment operates in part via a restriction in microsatellite

length, such that occasional deletions or internal point mutations lead to shorter and less polymorphic loci upon cross-species transfer (Vowles & Amos 2006). In a previous study of molecular properties recorded for a large number of microsatellites cross-amplified in birds, only the repeat number in the source species had a significant effect on cross-species polymorphism success (Primmer et al. 2005).

Conclusions

Our results indicate that cross-species transferability of microsatellite markers is unevenly distributed across taxa (Fig. 1A, B). High amplification success within and between genera in many groups of animals and plants indicates a great potential to use microsatellites and their flanking regions as a source of single- or low-copy nuclear sequences, as suggested by Zhang & Hewitt (2003). Of course, the likelihood of orthology vs. paralogy of cross-amplified loci will have to be evaluated on a case-by-case basis, e.g. based on the evolutionary information inherent in the growing number of complete genomic sequences available (Vision et al. 2000; Lynch & Conery 2003; Tuskan et al. 2006).

Variation between taxa is even greater when cross-species transfer success is evaluated in terms of marker polymorphism, the ultimate criterion for the direct use of microsatellite length polymorphisms as markers (Fig. 1B). In effect, tests for cross-species transferability of polymorphicmarkers can be expected to yield returns in most groups of animals within and between genera and even across dif-ferent families in some cases (> 40% transfer success in mammals, > 25% in fishes, and > 10% in birds at this level; Fig. 1B). By contrast, transferability of polymorphic mark-ers in plants is likely to be successful mainly within genera (success rate close to 60% in eudicots and close to 40% in the reviewed monocots). Between genera, transfer rates are approximately 10% for eudicots, and students of monocots such as orchids or grasses are very unlikely to get away without isolating novel markers from the genomes of new target genera. An exception, in our experience, are large adaptive radiations with low levels of DNA sequence divergence such as Bromeliaceae, where polymorphic markers are readily transferred between species of the same subfamily and beyond (Palma-Silva et al. 2006; Barbará et al. 2007).

Despite encouraging aspects, it is clear that the potentialfor cross-species transfer of microsatellites is more limited than molecular ecologists would wish for. Although EST-derived microsatellites may be conserved over larger evolu-tionary distances, their transfer beyond the genus level often appears to be limited too (Pashley et al. 2006; Bouck & Vision 2007). Also, molecular ecology studies increasingly aim at comparing genetic, demographic, behavioural, and breeding system parameters among related species ormultiple species co-occurring in the same community. This

Fig. 1 Mean values for the percentage of markers amplified (A) and, among those that amplified, percentage of markers polymorphic (B) across different taxonomic groups and taxonomic ranges of molecular marker assays for a total of 611 cross-species encounters from 64 studies. The taxonomic groups considered in the analysis are indicated by different colours. In addition, the following symbols help distinguish between major groups of taxa: filled circles for plants, filled rectangles for vertebrates, and filled triangles for invertebrates and fungi. The only mean value availablefor conifers (‘between species-within genus’ category) is not visible as it overlaps exactly with the values for fishes and fungi.

© 2007 The AuthorsJournal compilation © 2007 Blackwell Publishing Ltd

3764 BA R BA R A ET AL .

© 2007 The AuthorsJournal compilation © 2007 Blackwell Publishing Ltd

Table 4 anova of the effects of taxonomic group, taxonomic range of marker assay, mating system, geographical distribution, distribution range, and generation time, on the proportion of markers amplified across species

Source of variation*

General linear model

F P valued.f. SS MS

Taxonomic group† 7 151.02 21.57 7.97 0.000Taxonomic range of marker assay 3 279.67 93.22 34.42 0.000Mating system 2 25.05 12.53 4.63 0.011Geographical distribution 4 10.23 2.56 0.95 0.438Distribution range 2 4.10 2.05 0.76 0.470Generation time 1 17.01 17.01 6.28 0.013Error 298 807.04 2.71

The residuals were weighted by the number of markers assayed in each study. Percentage of variation explained by the entire model (R2) = 36%. Interaction effects were not tested. Significant main effects at the 0.05 level are indicated with bold type. *For factor levels of predictor variables see Table 2. †Reptiles and fungi were excluded from this analysis because of missing data for some of the variables. d.f.: degrees of freedom; SS: sums of squares; MS: mean squares.

Fig. 2 Effects of four different organismal or geographical factors on the proportion of markers amplified (means ± SE), adjusted for differences in the taxonomic range of cross-species transfer. X-axes, from top to bottom panel: mating system (primarily selfing, mixed, or outcrossing), geographical distribution (tropical, tropical-temperate, temperate, temperate-polar, or tropical-temperate-polar), distribution range (narrowly endemic regional), or widespread and generation time (annual/semelparous, or perennial/iteroparous). Y-axes: amplification success adjusted for differences in the taxonomic range of cross-species transfer.

CR O S S - S P EC I E S T R A N S F E R O F M I C RO S AT E LL I TE S 3765

raises issues of interspecific differences in mutation rates, constraints on microsatellite evolution, and homoplasy (Estoup & Cornuet 1999; Amos 1999). Several alternative sources of nuclear markers which may be more easily transferable are currently under development. These includeEST-derived single nucleotide polymorphisms and exon-primed, intron spanning markers (Bouck & Vision 2007), single-copy nuclear polymorphisms identified from whole genome sequences or genomic libraries (Zhang & Hewitt 2003), and nuclear DNA ‘barcodes’ potentially applicable across entire kingdoms (Chase et al. 2005). These develop-ments, in combination with the increasing efficiency and decreasing costs of DNA sequencing, raise the hope that molecular ecologists will soon have an upgraded ‘toolbox’ of transferable markers from which to choose.

Acknowledgements

We thank Kevin Livingstone, Loren Rieseberg, Alex Buerkle, Louis Bernatchez, Mark Chase, and Tim Barraclough for helpful discussions and feedback. This work was supported by fellow-ships from the Weston Foundation and Mellon Foundation to T.B. and C.P.S. and grants from the Brazilian Scientific Council (CNPq) to C.P.S. and G.M.P.

References

Amos W (1999) A comparative approach to the study of micro-satellite evolution. In: Microsatellites: Evolution and Applications

(eds Goldstein DB, Schlötterer C), pp. 66–79. Oxford University Press, Oxford, UK.

Barbará T, Martinelli G, Fay MF, Mayo SJ, Lexer C (2007) Popula-tion differentiation and species cohesion in two closely related plants adapted to neotropical high-altitude ‘inselbergs’, Alcantareaimperialis and A. geniculata. Molecular Ecology, 16, 1981–1992.

Belfiore NM, May B (2000) Variable microsatellite loci in red swamp crayfish, Procambarus clarkii, and their characterization in other crayfish taxa. Molecular Ecology, 9, 2230–2234.

Blum MJ, Sloop CM, Ayres DR, Strong DR (2004) Characteriza-tion of microsatellite loci in Spartina species (Poaceae). Molecular Ecology Notes, 4, 39–42.

Bouck A, Vision T (2007) The molecular ecologist’s guide to expressed sequence tags. Molecular Ecology, 16, 907–924.

Cairney M, Taggart JB, Høyheim B (2000) Characterization of microsatellite and minisatellite loci in Atlantic salmon (Salmo salar L.) and cross-species amplification in other salmonids. Molecular Ecology, 9, 2175–2178.

Chagne D, Chaumeil P, Ramboer A et al. (2004) Cross-species transferability and mapping of genomic and cDNA SSRs in pines. Theoretical and Applied Genetics, 109, 1204–1214.

Chase MW, Salamin N, Wilkinson M et al. (2005) Land plants and DNA barcodes: short-term and long-term goals. Philosophical Transactions of the Royal Society of London. Series B, BiologicalSciences, 360, 1889–1895.

Chbel F, Broderick D, Idaghdour Y, Korrida A, McCormick P (2002) Characterization of 22 microsatellites loci from the endangeredHoubara bustard (Chlamydotis undulata undulata). Molecular Ecology Notes, 2, 484–487.

Combes MC, Andrzejewski S, Anthony F et al. (2000) Characteri-zation of microsatellite loci in Coffea arabica and related coffee species. Molecular Ecology, 9, 1178–1180.

Coulibaly I, Gharbi K, Danzmann RG, Yao J, Rexroad CE (2005) Characterization and comparison of microsatellites derived from repeat-enriched libraries and expressed sequence tags. Animal Genetics, 36, 309–315.

Daly D, Archer ME, Watts PC et al. (2002) Polymorphic micro-satellite loci for eusocial wasps (Hymenoptera: Vespidae). Molecular Ecology Notes, 2, 273–275.

Dawson DA, Bretman AJ, Tregenza T (2003) Microsatellite loci for the field cricket, Gryllus bimaculatus and their cross-utility in other species of Orthoptera. Molecular Ecology Notes, 3, 191–195.

Dawson DA, Hunter FM, Pandhal J et al. (2005) Assessment of 17 new whiskered auklet (Aethia pygmaea) microsatellite loci in 42 seabirds identifies 5–15 polymorphic markers for each of nine Alcinae species. Molecular Ecology Notes, 5, 289–297.

Dawson DA, Rossiter SJ, Jones G, Faulkes CG (2004) Microsatel-lite loci for the greater horseshoe bat, Rhinolophus ferrumequinum(Rhinolophidae, Chiroptera) and their cross-utility in 17 other bat species. Molecular Ecology Notes, 4, 96–100.

Eackles MS, King TL (2002) Isolation and characterization of microsatellite loci in Lampsilis abrupta (Bivalvia: Unionidae) and cross-species amplification within the genus. Molecular Ecology Notes, 2, 559–562.

Ellegren H, Primmer CR, Sheldon BC (1995) Microsatelliteevolution — directionality or bias. Nature Genetics, 11, 360–362.

Escribano P, Viruel MA, Hormaza JI (2004) Characterization and cross-species amplification of microsatellite markers in cher-imoya (Annona cherimola Mill., Annonaceae). Molecular Ecology Notes, 4, 746–748.

Estoup A, Cornuet J-M (1999) Microsatellite evolution: inferences

Fig. 3 The relationship between amplification success and the ratio of genome size (C value) between target and source species in 45 cases for which genome size estimates were available for both target and source, including plants, fishes, one bird and one insect. Amplification success decreases with increasing genome size in the target species relative to the source. X-axis: genomesize ratio. Y-axes: arcsine-transformed percentages of amplified markers. ‘A′ and ‘C’ denote the only available entries for birds (Anatidae) and insects (Culicidae), respectively.

© 2007 The AuthorsJournal compilation © 2007 Blackwell Publishing Ltd

3766 BA R BA R A ET AL .

from population data. In: Microsatellites. Evolution and Applications(eds Goldstein DB, Schlötterer C), pp. 49–65. Oxford University Press, Oxford, UK.

Farias IP, Hrbek T, Brinkmann H, Sampaio I, Meyer A (2003) Characterization and isolation of DNA microsatellite primers for Arapaima gigas, an economically important but severely over-exploited fish species of the Amazon basin. MolecularEcology Notes, 3, 128–130.

Feulner PGD, Kirschbaum F, Tiedemann R (2005) Eighteenmicrosatellite loci for endemic African weakly electric fish (Campylomormyrus, Mormyridae) and their cross species appli-cability among related taxa. Molecular Ecology Notes, 5, 446–448.

Flanagan NS, Blum MJ, Davison A et al. (2002) Characterization of microsatellite loci in neotropical Heliconius butterflies. Molecular Ecology Notes, 2, 398–401.

Flanagan NS, Ebert D, Porter C, Rossetto M, Peakall R (2006) Micro-satellite markers for evolutionary studies in the sexually deceptive orchid genus Chiloglottis. Molecular Ecology Notes, 6, 123–126.

Funk CR, Schmid-Hempel R, Schmid-Hempel P (2006) Micro-satellite loci for Bombus spp. Molecular Ecology Notes, 6, 83–86.

Garner TWJ (2002) Genome size and microsatellites: the effect of nuclear size on amplification potential. Genome, 45, 212–215.

Gaur A, Singh A, Arunabala V et al. (2003) Development and characterization of 10 novel microsatellite markers from Chital deer (Cervus axis) and their cross-amplification in other related species. Molecular Ecology Notes, 3, 607–609.

Gemmell NJ, Allen PJ, Goodman SJ, Reed JZ (1997) Interspecific microsatellite markers for the study of pinniped populations. Molecular Ecology, 6, 661–666.

Gillooly JF, Allen AP, West GB, Brown JH (2005) The rate of DNA evolution: effects of body size and temperature on the molecular clock. Proceedings of the National Academy of Sciences, USA, 102, 140–145.

Gunn MR, Dawson DA, Leviston A et al. (2005) Isolation of 18 polymorphic microsatellite loci from the North American red squirrel, Tamiasciurus hudsonicus (Sciuridae, Rodentia), and theircross-utility in other species. Molecular Ecology Notes, 5, 650–653.

Hale ML, Squirrell J, Borland AM, Wolff K (2002) Isolation ofpolymorphic microsatellite loci in the genus Clusia (Clusiaceae). Molecular Ecology Notes, 2, 506–508.

Higgins K, Lynch L (2001) Metapopulation extinction caused by mutation accumulation. Proceedings of the National Academy of Sciences, USA, 98, 2928–2933.

Holmen J, Vollestad LA, Jakobsen KS, Primmer CR (2005) Cross-species amplification of zebrafish and central stonerollermicrosatellite loci in six other cyprinids. Journal of Fish Biology, 66, 851–859.

Huttunen S, Schotterer C (2002) Isolation and characterization of microsatellites in Drosophila virilis and their cross species amplification in members of the D. virilis group. MolecularEcology Notes, 2, 593–597.

Iyengar A, Piyapattanakorn S, Heipel DA et al. (2000) A suite of highly polymorphic microsatellite markers in turbot (Scoph-thalmus maximus L.) with potential for use across several flatfish species. Molecular Ecology, 9, 368–371.

Jones RC, Vaillancourt RE, Jordan GJ (2004) Microsatellites for use in Nothofagus cunninghamii (Nothofagaceae) and related species. Molecular Ecology Notes, 4, 14–16.

Keeney DB, Heist EJ (2003) Characterization of microsatellite loci isolated from the blacktip shark and their utility in requiem and hammerhead sharks. Molecular Ecology Notes, 3, 501–504.

Lanaud C, Risterucci AM, Pieretti I et al. (1999) Isolation and

characterization of microsatellites in Theobroma cacao L. Molecular Ecology, 8, 2141–2143.

Lim KY, Kovarik A, Matyasek R et al. (2007) The sequence of events leading to Nicotiana genome turnover in less than five million years. New Phytologist. doi: 10.1111/j.1469-8137.2007.02121.x

Lippe C, Dumont P, Bernatchez L (2004) Isolation and identificationof 21 microsatellite loci in the copper redhorse (Moxostoma hubbsi; Catostomidae) and their variability in other catostomids. Molecular Ecology Notes, 4, 638–641.

Lynch M, Conery JS (2003) The origins of genome complexity. Science, 302, 1401–1404.

Maak S, Wimmers K, Weigend S, Neumann K (2003) Isolation and characterization of 18 microsatellites in the Peking duck (Anas platyrhynchos) and their application in other waterfowl species. Molecular Ecology Notes, 3, 224–227.

Martinez-Cruz B, David VA, Godoy JA et al. (2002) Eighteen poly-morphic microsatellite markers for the highly endangered Spanish imperial eagle (Aquila adalberti) and related species. Molecular Ecology Notes, 2, 323–326.

Maudet C, Beja-Pereira A, Zeyl E et al. (2004) A standard set of polymorphic microsatellites for threatened mountain ungulates(Caprini, Artiodactyla). Molecular Ecology Notes, 4, 49–55.

Mavarez J, Gonzalez M (2006) A set of microsatellite markers for Heliconius melpomene and closely related species. MolecularEcology Notes, 6, 20–23.

McMullin ER, Wood J, Hamm S (2004) Twelve microsatellites for two deep sea polychaete tubeworm species, Lamellibrachia luymesi and Seepiophila jonesi, from the Gulf of Mexico. Molecular Ecology Notes, 4, 1–4.

McRae SB, Emlen ST, Rubenstein DR, Bogdanowicz SM (2005) Polymorphic microsatellite loci in a plural breeder, the grey-capped social weaver (Pseudonigrita arnaudi), isolated with an improved enrichment protocol using fragment size-selection. Molecular Ecology Notes, 5, 16–20.

Mohra C, Fellendorf M, Segelbacher G, Paxton RJ (2000) Dinu-cleotide microsatellite loci for Andrena vaga and other andrenid bees from non-enriched and CT-enriched libraries. Molecular Ecology, 9, 2189–2192.

Morillo E, Second G, Pham JL, Risterucci AM (2004) Development of DNA microsatellite markers in the Andean root crop arracacha: Arracacia xanthorrhiza Banc. (Apiaceae). Molecular Ecology Notes, 4, 680–682.

Myers N, Mittermeier RA, Mittermeier CG, da Fonseca GAB, Kent J (2000) Biodiversity hotspots for conservation priorities. Nature, 403, 853–858.

Noor MAF, Feder JL (2006) Speciation genetics: evolving approaches. Nature Reviews Genetics, 7, 851–861.

Ortega J, Maldonado JE, Arita HT, Wilkinson GS, Fleischer RC (2002) Characterization of microsatellite loci in the Jamaican fruit-eating bat Artibeus jamaicensis and cross-species amplification. Molecular Ecology Notes, 2, 462–464.

Ovenden JR, Street R, Broderick D (2006) New microsatellite loci for carcharhinid sharks (Carcharhinus tilstoni and C. sorrah) and their cross-amplification in other shark species. Molecular Eco-logy Notes, 6, 415–418.

Palma-Silva C, Cavallari MM, Barbará T et al. (2006) A set of poly-morphic microsatellite loci for Vriesea gigantea and Alcantarea imperialis(Bromeliaceae) and cross-amplification in other bromeliad species. Molecular Ecology Notes. doi: 10.1111/j.1471-8286.2006.01665.x.

Pashley CH, Ellis JR, McCauley DE, Burke JM (2006) EST data-bases as a source for molecular markers: lessons from Helianthus. Journal of Heredity, 97, 381–388.

© 2007 The AuthorsJournal compilation © 2007 Blackwell Publishing Ltd

CR O S S - S P EC I E S T R A N S F E R O F M I C RO S AT E LL I TE S 3767

Perez JO, Dambier D, Ollitrault P et al. (2006) Microsatellitemarkers in Carica papaya L. isolation, characterization and transferability to Vasconcellea species. Molecular Ecology Notes, 6, 212–217.

Perry GML, King TL, St-Cyr J, Valcourt M (2005) Isolation and cross-familial amplification of 41 microsatellites for the brook charr (Salvelinus fontinalis). Molecular Ecology Notes, 5, 346–351.

Porter C, Rymer PD, Rossetto M (2006) Isolation and character-ization of microsatellite markers for the waratah, Telopeaspeciosissima (Proteaceae). Molecular Ecology Notes, 6, 446–448.

Primmer CR, Merilä J (2002) A low rate of cross-species micro-satellite amplification success in ranid frogs. Conservation Genetics, 3, 445–449.

Primmer CR, Møller AP, Ellegren H (1996) A wide-range survey of cross-species microsatellite amplification in birds. Molecular Ecology, 5, 365–378.

Primmer CR, Painter JN, Koskinen MT, Palo JU, Merilä J (2005) Factors affecting avian cross-species microsatellite amplification. Journal of Avian Biology, 36, 348–360.

Richardson DS, Jury FL, Dawson DA et al. (2000) Fifty Seychelles warbler (Acrocephalus sechellensis) microsatellite loci poly-morphic in Sylviidae species and their cross-species amplifi-cation in other passerine birds. Molecular Ecology, 9, 2225–2230.

Rodriguez F, Rexroad CE, Palti Y (2003) Characterization of twenty-four microsatellite markers for rainbow trout (Onco-rhynchus mykiss). Molecular Ecology Notes, 3, 619–622.

Rogers SM, Marchand MH, Bernatchez L (2004) Isolation, charac-terization and cross-salmonid amplification of 31 microsatellite loci in the lake whitefish (Coregonus clupeaformis, Mitchill). Molecular Ecology Notes, 4, 89–92.

Rosetto M (2001) Sourcing of SSR markers from related plant species. In: Plant Genotyping: The DNA Fingerprinting of Plants(ed. Henry RJ), pp. 211–224. CAB International, Oxford, UK.

Rubenstein DR (2005) Isolation and characterization of polymorphic microsatellite loci in the plural cooperatively breeding superbstarling, Lamprotornis superbus. Molecular Ecology Notes, 5, 739–744.

Salywon A, Dierig DA (2006) Isolation and characterization of microsatellite loci in Lesquerella fendleri (Brassicaceae) and cross-species amplification. Molecular Ecology Notes, 6, 382–384.

Schlötterer C, Amos W, Tautz D (1991) Conservation of polymor-phic simple sequence loci in cetacean species. Nature, 354, 63–65.

Schug MD, Regulski EE, Pearce A, Smith SG (2004) Isolation and characterization of dinucleotide repeat microsatellites in Drosophila ananassae. Genetical Research, 83, 19–29.

Shearman DCA, Gilchrist AS, Crisafulli D et al. (2006) Micro-satellite markers for the pest fruit fly, Bactrocera papayae (Diptera: Tephritidae) and other Bactrocera species. Molecular Ecology Notes, 6, 4–7.

Sinclair EA, Scholl R, Bezy RL, Crandall KA, Sites JW (2006) Isolation and characterization of di- and tetranucleotide micro-satellite loci in the yellow-spotted night lizard Lepidophymaflavimaculatum (Squamata: Xantusiidae). Molecular Ecology Notes, 6, 233–236.

Slippers B, Burgess T, Wingfield BD et al. (2004) Development of simple sequence repeat markers for Botryosphaeria spp. with Fusicoccum anamorphs. Molecular Ecology Notes, 4, 675–677.

Smith JL, Keyghobadi N, Matrone MA, Escher RL, Fonseca DM (2005) Cross-species comparison of microsatellite loci in the Culex pipienscomplex and beyond. Molecular Ecology Notes, 5, 697–700.

Squirrell J, Wolff K (2001) Isolation of polymorphic microsatellite loci in Plantago major and P. intermedia. Molecular Ecology Notes, 1, 179–181.

Steinkellner H, Lexer C, Turetschek E, Glossl J (1997) Conservation of (GA)n microsatellite loci between Quercus species. Molecular Ecology, 6, 1189–1194.

Terui H, Lian CL, Saito Y, Ide Y (2006) Development of micro-satellite markers in Acer capillipes. Molecular Ecology Notes, 6, 77–79.

Tonnis BD (2006) Microsatellite DNA markers for the rainbow darter, Etheostoma caeruleum (Percidae), and their potential utility for other darter species. Molecular Ecology Notes, 6, 230–232.

Topinka JR, Donovan AJ, May B (2004) Characterization of micro-satellite loci in Kearney’s bluestar (Amsonia keameyana) and cross-amplification in other Amsonia species. Molecular Ecology Notes, 4, 710–712.

Tostain S, Scarcelli N, Brottier P et al. (2006) Development of DNA microsatellite markers in tropical yam (Dioscorea sp.). Molecular Ecology Notes, 6, 173–175.

Tuskan GA, DiFazio S, Jansson S, Bohlmann J, Grigoriev I, HellstenU (2006) The genome of black cottonwood, Populus trichocarpa(Torr. & Gray). Science, 313, 1596–1604.

Vasemagi A, Nilsson J, Primmer CR (2005) Seventy-five EST-linked Atlantic salmon (Salmo salar L.) microsatellite markers and their cross-amplification in five salmonid species. Molecular Ecology Notes, 5, 282–288.

Vision TJ, Brown DG, Tanksley SD (2000) The origins of genomic duplications in Arabidopsis. Science, 290, 2114–2117.

Vowles EJ, Amos W (2006) Quantifying ascertainment bias and species-specific length differences in human and chimpanzee microsatellites using genome sequences. Molecular Biology and Evolution, 23, 598–607.

Wadud MA, Lian CL, Nara K, Ishida TA, Hogetsu T (2006) Devel-opment of microsatellite markers from an ectomycorrhizal fungus,Laccaria amethystina, by a dual-suppression-PCR technique. Molecular Ecology Notes, 6, 130–132.

White G, Powell W (1997) Cross-species amplification of SSR loci in the Meliaceae family. Molecular Ecology, 6, 1195–1197.

Whitham TG, Bailey JK, Schweitzer JA et al. (2006) A framework for community and ecosystem genetics: from genes to ecosystems. Nature Reviews Genetics, 7, 510–523.

Williamson JE, Huebinger RM, Sommer JA, Louis EE, Barber RC(2002) Development and cross-species amplification of 18microsatellite markers in the Sumatran tiger (Panthera tigris sumatrae). Molecular Ecology Notes, 2, 110–112.

Yue GH, Kovacs B, Orban L (2003) Microsatellites from Clariasbatrachus and their polymorphism in seven additional catfish species. Molecular Ecology Notes, 3, 465–468.

Zhang D-X, Hewitt GM (2003) Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects. Molecular Ecology, 12, 563–584.

Zhu Y, Landi M, Queller DC, Turillazzi S, Strassmann JE (2000) Polymorphic microsatellite loci for primitively eusocial steno-gastrine wasps. Molecular Ecology, 9, 2203–2205.

Thelma Barbará, Clarisse Palma-Silva, and Gecele M. Paggi are currently PhD students working on various aspects of population genetics, microevolution, phylogeography, and species delimitationin neotropical plant species of the Bromeliaceae family. Fernanda Bered is group leader of the bromeliad conservation genetics team at UFRGS in Porto Alegre, Brazil. Christian Lexer, who has initiated and coordinated this literature work, is the population geneticist in Mike Fay’s Genetics section in the Jodrell Laboratory at RBG Kew in the U.K.

© 2007 The AuthorsJournal compilation © 2007 Blackwell Publishing Ltd